Configuring .blend file for remote machine GPU rendering
As far as I understood, you manually put your .blend file on the server without using any third-party software. This answer so may help you:

How do I force the netrender to render everything on GPU?

This consists of running blender from the command line while also passing him a python script to set the GPU device (code from the link above):

blender -b file.blend -E CYCLES -t 0 -o //file -P script.py


This way you CAN set GPU rendering from the command line using, in the python script, bpy.context.scene.cycles.device = 'GPU'.